Detailed information of TA system TA038180

Bioinformatically predicted

Overview

TA module

• Type: II
• Classification (family/domain): vapBC/LOTUS_5_Limkain_b1-VagC
• Location: 4544267..4544919
• Replicon: chromosome
• Accession: NZ_AP024238
• Organism: Rhodoferax sp. MIZ03

Toxin (Protein)

• Gene name: vapC
• Uniprot ID: -
• Locus tag: LDN84_RS20945
• Protein ID: WP_223905573.1
• Coordinates: 4544515..4544919 (+)
• Length: 135 a.a.

Antitoxin (Protein)

• Gene name: vapB
• Uniprot ID: -
• Locus tag: LDN84_RS20940
• Protein ID: WP_223905571.1
• Coordinates: 4544267..4544518 (+)
• Length: 84 a.a.

Genomic Context

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
LDN84_RS20910 (MIZ03_4410)	4539724..4540698	+	975	WP_223905560.1	MlaD family protein	-
LDN84_RS20915 (MIZ03_4411)	4540738..4541460	+	723	WP_223905562.1	ABC-type transport auxiliary lipoprotein family protein	-
LDN84_RS20920 (MIZ03_4412)	4541522..4542232	+	711	WP_223905564.1	glutathione S-transferase N-terminal domain-containing protein	-
LDN84_RS20925 (MIZ03_4413)	4542235..4542855	+	621	WP_223905566.1	glutathione S-transferase family protein	-
LDN84_RS20930 (MIZ03_4414)	4543081..4543500	-	420	WP_223905568.1	hypothetical protein	-
LDN84_RS20935 (MIZ03_4415)	4543570..4543992	-	423	WP_223905569.1	HTH domain-containing protein	-
LDN84_RS20940 (MIZ03_4416)	4544267..4544518	+	252	WP_223905571.1	AbrB/MazE/SpoVT family DNA-binding domain-containing protein	Antitoxin
LDN84_RS20945 (MIZ03_4417)	4544515..4544919	+	405	WP_223905573.1	type II toxin-antitoxin system VapC family toxin	Toxin
LDN84_RS20950 (MIZ03_4418)	4545026..4546261	-	1236	WP_223905575.1	glycolate oxidase subunit GlcF	-
LDN84_RS20955 (MIZ03_4419)	4546266..4547414	-	1149	WP_223905577.1	glycolate oxidase subunit GlcE	-
LDN84_RS20960 (MIZ03_4420)	4547550..4547855	-	306	WP_223905579.1	YqjK family protein	-
LDN84_RS20965 (MIZ03_4421)	4547845..4548234	-	390	WP_223905581.1	phage holin family protein	-
LDN84_RS20970 (MIZ03_4422)	4548239..4548550	-	312	WP_223905583.1	DUF883 family protein	-
LDN84_RS20975 (MIZ03_4423)	4548666..4549574	-	909	WP_223913222.1	SMP-30/gluconolactonase/LRE family protein	-

Associated MGEs

MGE detail	Similar MGEs	Relative position	MGE Type	Cargo ARG	Virulence gene	Coordinates	Length (bp)

Relative position:
(1) inside: TA loci is completely located inside the MGE;
(2) overlap: TA loci is partially overlapped with the MGE;
(3) flank: The TA loci is located in the 5 kb flanking regions of MGE.

Domains

Predicted by InterproScan

Toxin

• PIN domain (5-125)

Antitoxin

No domain identified.

Sequences

Toxin

Protein

• Length: 135 a.a.
• Molecular weight: 15013.32 Da
• Isoelectric Point: 5.1599

>T38180 WP_223905573.1 NZ_AP024238:4544515-4544919 [Rhodoferax sp. MIZ03]
MRPRYMLDTNVVSHIMQGRDAELLARLTQVPVGQVVMSSVTLAELEYGLHRKGQPVRLRNALTQVLLRIDVLPWDEDVAT
CYGEFCATLEAQGINLSDFDMMIAAHAVAADSTLVSRDKAFAQVNGERLRLEIW

Nucleotide

• Length: 405 bp

>T38180 NZ_AP024238:4544515-4544919 [Rhodoferax sp. MIZ03]
ATGAGGCCGCGCTACATGCTCGACACCAATGTGGTCAGCCACATCATGCAGGGGCGCGATGCCGAGTTGCTGGCTCGCTT
GACGCAGGTGCCGGTGGGGCAAGTGGTGATGTCCAGCGTGACCTTGGCCGAGTTGGAATACGGCTTGCACCGCAAAGGGC
AACCTGTTCGCTTGCGAAATGCCCTGACACAAGTGCTGCTGCGTATCGACGTGCTGCCGTGGGATGAGGACGTAGCAACT
TGTTATGGCGAGTTTTGCGCCACGCTGGAGGCCCAAGGCATCAACCTCAGTGACTTTGACATGATGATCGCCGCCCATGC
CGTAGCGGCGGATTCCACCCTGGTCAGCCGCGACAAGGCGTTTGCGCAGGTGAACGGGGAACGCTTGAGGCTGGAGATTT
GGTAA

Antitoxin

Protein

• Length: 84 a.a.
• Molecular weight: 9732.02 Da
• Isoelectric Point: 6.3409

>AT38180 WP_223905571.1 NZ_AP024238:4544267-4544518 [Rhodoferax sp. MIZ03]
MRQTAKIFVTGRSQAVRLPLEFRFDVSEVFIRRDALTGDVVLSRKPTDWQGLLDVVAQNKDEDLLVERRQTQARRDPFEG
WQE

Nucleotide

• Length: 252 bp

>AT38180 NZ_AP024238:4544267-4544518 [Rhodoferax sp. MIZ03]
ATGCGTCAGACTGCCAAAATTTTCGTCACCGGCCGCAGCCAGGCGGTTCGCTTGCCGCTGGAGTTTCGCTTTGACGTGTC
AGAAGTATTCATCCGCCGCGATGCCCTCACGGGTGATGTGGTGCTGTCGCGTAAACCCACGGATTGGCAAGGCCTGCTGG
ATGTGGTGGCTCAAAACAAAGACGAAGACTTGTTGGTTGAGCGCCGCCAAACCCAGGCGCGGCGCGACCCTTTTGAGGGC
TGGCAGGAATGA